Philippines President Rodrigo Duterte told Malaysia and Indonesia to bomb fleeing Filipino militants carrying out kidnappings together with their hostages.

Duterte justified that the hostages too should be bombed as they "are not supposed to be there", according to the Associated Press.

The report quoted Duterte as saying that he conveyed this message to both Malaysian Prime Minister Najib Abdul Razak and Indonesian President Joko Widodo (Jokowi).

"Bomb them. If they cannot be captured you bomb them.

"How about the hostages? Eh, bomb them also. They're not supposed to be there, there is a warning," he was quoted as saying.

There has been a spat of kidnappings off Sabah waters, many of whom taken as hostages were Malaysians, Indonesians or international tourists.

Militants have used Southern Philippines as a launchpad, taking hostages in Sabah for ransom.

Last month, Manila granted Malaysian security forces permission to pursue the militants into Philippines waters.

On Thursday, three suspected kidnappers were shot dead by Malaysian security forces off Sabah waters.